Home

Pinball

Pinball is a new assembler tool that analyses ChIP-seq and other enrichment-based short read datasets into peaks which can be studied per se or mapped to sequenced genomes that are evolutionarily close in the phylogenetic tree. The resulting peaks can also be compared directly in different species to study the evolution of epigenomic marks (e.g. histone marks), protein-DNA interactions (e.g. transcription factors), protein-RNA interactions (e.g. HITS-CLIP experiments), small RNAs, chromatin interactions, etc.

Pinball can also be used to assess the enrichment quality of any newly sequenced library from any enrichment-based technology (ChIP-seq, HITS-CLIP, Chia-PET, small RNAs, sequence-capture targeted-sequencing, etc), even if the purpose is to finally map the reads to the genome reference. This use of the program gives read-read overlap statistics that are unbiased towards assembled genomes and calculates what fraction of reads are found together as clusters that will likely become part of TFBS peaks, miRNAs or miRNA target sites, Chia-PET chromatin interaction events, single exons in an exome study, and so forth. In addition, the range of cluster sizes is provided, which estimates the intensity or coverage spectrum of ChIP-seq peaks, levels of repetitiveness and saturation levels of sequence capture analysis.

Download

Pinball can be downloaded here: ftp://ftp.ebi.ac.uk/pub/databases/ensembl/avilella/pinball/

The pinball-{version}.tar.gz bundle includes the core functionality and some third-party tools.

The Pinball-machine-{version}.ova image is a Pinball virtual machine ready to use with all installed binaries and several accompanying and third-party tools.